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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: X-108084978-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108084978&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 108084978,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002814.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Gly226Asp",
"transcript": "NM_002814.4",
"protein_id": "NP_002805.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 226,
"cds_start": 677,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000217958.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002814.4"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Gly226Asp",
"transcript": "ENST00000217958.8",
"protein_id": "ENSP00000217958.3",
"transcript_support_level": 1,
"aa_start": 226,
"aa_end": null,
"aa_length": 226,
"cds_start": 677,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002814.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000217958.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.*142G>A",
"hgvs_p": null,
"transcript": "ENST00000361815.9",
"protein_id": "ENSP00000354906.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": null,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361815.9"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Gly226Asp",
"transcript": "ENST00000923416.1",
"protein_id": "ENSP00000593475.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 226,
"cds_start": 677,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923416.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Gly197Asp",
"transcript": "ENST00000923417.1",
"protein_id": "ENSP00000593476.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 197,
"cds_start": 590,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923417.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.578G>A",
"hgvs_p": "p.Gly193Asp",
"transcript": "ENST00000340200.5",
"protein_id": "ENSP00000345963.5",
"transcript_support_level": 3,
"aa_start": 193,
"aa_end": null,
"aa_length": 193,
"cds_start": 578,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000340200.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Gly185Asp",
"transcript": "ENST00000372295.5",
"protein_id": "ENSP00000361369.1",
"transcript_support_level": 5,
"aa_start": 185,
"aa_end": null,
"aa_length": 185,
"cds_start": 554,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372295.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.530G>A",
"hgvs_p": "p.Gly177Asp",
"transcript": "ENST00000853188.1",
"protein_id": "ENSP00000523247.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 177,
"cds_start": 530,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000853188.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.431G>A",
"hgvs_p": "p.Gly144Asp",
"transcript": "ENST00000946898.1",
"protein_id": "ENSP00000616957.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 144,
"cds_start": 431,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946898.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.*142G>A",
"hgvs_p": null,
"transcript": "NM_170750.3",
"protein_id": "NP_736606.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": null,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_170750.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"hgvs_c": "c.*142G>A",
"hgvs_p": null,
"transcript": "ENST00000372296.5",
"protein_id": "ENSP00000361370.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 110,
"cds_start": null,
"cds_end": null,
"cds_length": 333,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372296.5"
}
],
"gene_symbol": "PSMD10",
"gene_hgnc_id": 9555,
"dbsnp": "rs140450722",
"frequency_reference_population": 0.00042471668,
"hom_count_reference_population": 149,
"allele_count_reference_population": 509,
"gnomad_exomes_af": 0.000391174,
"gnomad_genomes_af": 0.000750188,
"gnomad_exomes_ac": 425,
"gnomad_genomes_ac": 84,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003871917724609375,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.07,
"revel_prediction": "Benign",
"alphamissense_score": 0.1229,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.358,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002814.4",
"gene_symbol": "PSMD10",
"hgnc_id": 9555,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Gly226Asp"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}